● EDU reduces O3 sensitivity of alfalfa by mediating antioxidant enzyme activities.
● AM symbiosis increases stomatal conductance and plant O3 sensitivity.
● AM fungi increase stomatal conductance by increasing plant stomatal density.
● AM inoculation combined with EDU can mitigate negative effects of O3 on plants.
Ozone (O3) is a phytotoxic air pollutant, both ethylenediurea (EDU) and arbuscular mycorrhizal (AM) fungi can affect plant O3 sensitivity. However, the underlying mechanisms of EDU and AM fungi on plant O3 sensitivity are unclear, and whether the combined application of the two can alleviate O3 damage has not been verified. In this study, an open-top chamber experiment was conducted to examine the effects of EDU and AM inoculation on growth and physiological parameters of alfalfa (Medicago sativa L.) plants under O3 enrichment. The results showed that EDU significantly decreased O3 visible injury (28.67%−68.47%), while AM inoculation significantly increased O3 visible injury. Mechanistically, the reduction of plant O3 sensitivity by EDU was mediated by antioxidant enzyme activities rather than stomatal conductance. Although AM inoculation increased antioxidant enzyme activities (4.99%−211.23%), it significantly increased stomatal conductance (42.69%) and decreased specific leaf weight (12.98%), the negative impact was overwhelming. Therefore, AM inoculation increased alfalfa’s O3 sensitivity. Furthermore, we found AM inoculation increased stomatal conductance by increasing stomatal density. The research indicated EDU was sufficient to counteract the negative effects of AM inoculation on O3 sensitivity. The combined application of EDU and AM fungi could largely alleviate the adverse effects of O3 on plant performance.
● Soil pH was the key factor influencing the phoD -harboring bacterial networks.
● Identification of a cluster positively linked to ALP activity and plant P uptake.
● Low soil pH resulted in a severe loss of phoD -harboring bacterial core cluster.
Fertilization treatments profoundly influence the bacterial communities associated with soil organic phosphorus (P) mineralization and alkaline phosphatase (ALP) activity. However, the relationships among the phoD-harboring bacterial communities associated with soil organic P mineralization, soil ALP activity, and plant P uptake under long-term fertilization remain unexplored. This study investigated these associations at the wheat rapid growth stage in a 40-year fertilization experiment. NPK fertilization led to a significant decrease in the diversity of phoD-harboring bacteria, which could be partially mitigated by the addition of organic materials. Soil pH emerged as the key factor influencing the structure and diversity of the phoD-harboring bacterial community. Furthermore, fertilizations involving manure additions resulted in more stable and cooperative phoD-harboring bacterial co-occurrence networks, compared to NPK fertilization. A functional phoD-harboring bacterial cluster, comprising genera Nostoc, Bradyrhizobium, and Pseudomonas, was identified, showing a positive association with soil ALP activity and plant P uptake. In summary, our study highlights the significant role of the identified core cluster of phoD-harboring bacteria in maintaining soil ALP activity and promoting plant P uptake, in decades of fertilization. Moreover, this study inferred a list of phoD-harboring bacterial genera from the core cluster, with established links to both plant P uptake and soil organic P mineralization. These findings offer valuable insights for sustainable agricultural practices.
● Ant morphological traits (dry mass, head length, body size and leg length) increased with elevation.
● Ant δ13C increased with elevation, whereas δ15N did not.
● Ant δ13C values correlated positively with soil C:N ratio.
Understanding the responses of species to changing climates is becoming increasingly urgent. Investigating the effects of climate change on the functional traits of species at the intraspecific level is particularly important. We used elevation gradients as proxies for climate change to explore the intraspecific responses of two ground-dwelling ant species, Ectomomyrmex javanus and Odontoponera transversa, from 100 to 700 m.a.s.l. within a subtropical evergreen broadleaf forest. Our study addressed the specific relationships among environmental factors, trait variations, and trophic levels. Key functional traits such as dry mass, head length, body size, and leg length exhibited a general increase with elevation. Using stable isotope signatures (δ13C and δ15N), we quantified shifts in diets and trophic positions along the elevation gradients. Notably, our data revealed a significant elevation-related increase in Ant δ13C, whereas δ15N exhibited no such correlation. Moreover, Ant δ13C values of E. javanus demonstrated a negative correlation with mean annual temperature (MAT), and the δ13C values of both species correlated positively with soil C:N ratio. Having revealed that the individual traits and δ13C signatures of ground-dwelling ants exhibit significant negative correlations with temperature, our findings suggest that climate warming has the potential to cause intraspecific variation in the functional traits and diets of ground-dwelling ants and possibly other insect species.
● Loquat orchard location was the main driver of microbial communities and loquat fruit quality.
● The average fruit weight was correlated with the ɑ- and β-diversity of bacteria and protists.
● Soil bacterial and protistan communities drove the multiple nutrient cycling.
The role of the soil microbiome in fruit quality within loquat orchards remains largely unknown. In this study, we collected soil samples from various loquat orchards in Ningbo, Zhejiang Province, China and investigated bacterial, fungal, and protist communities. The results showed that soil physicochemical conditions, the microbial community, and loquat fruit quality were significantly related to orchard location but unrelated to cultivation time and fertilization. The heterogeneity of the bacterial community was driven by soil pH, available phosphorus, and available potassium (AK). The fungal community was driven by soil electrical conductivity and AK. The protist community was driven by soil dissolved organic nitrogen and AK. The average fruit weight was significantly correlated with the ɑ- and β-diversity of bacteria and protists as well as the soil multiple nutrient cycling index. Several microbial phyla were related to average fruit weight, while other fruit quality indicators could not be explained by the soil microbiome. Our results reveal that bacterial and protist communities in loquat orchards drive the cycling of multiple nutrients that are related to fruit weight. These insights shed light on the relationship among the soil microbiome, nutrient cycling, and fruit quality, offering valuable scientific guidance for orchard management practices.
● Agricultural activities may promote the conversion of inorganic Hg to MeHg in soil.
● Hg and As present an extremely and a moderately contaminated level, respectively.
● The human health risks posed by As, Hg, and Ni merit more attention.
● Pokeweed may be considered as a potential Hg hyperaccumulator.
Soil pollution caused by potentially toxic metal(loid)s (PTMs) near mercury (Hg) mines has attracted extensive attention, yet the status and potential health risks of PTM contamination in soils near Hg mining sites have rarely been investigated on a large scale. Global data on methylmercury (MeHg), Hg, Cd, Cr, As, Pb, Cu, Zn, Mn, and Ni concentrations in soils from Hg mining areas were obtained from published research articles (1999–2023). Based on the database, pollution levels, spatial distributions, and potential health risks were investigated. Results indicated that the average percentage of MeHg to total Hg in agricultural soils (0.19%) was significantly higher than that in non-agricultural soils (0.013%). Indeed, 72.4% of these study sites were extremely contaminated with Hg. Approximately 45% of the examined sites displayed a moderate level of As contamination or even more. Meanwhile, the examined sites in Spain and Turkey exhibited considerably higher pollution levels of Hg and As than other regions. The mean hazard indices of the nine PTMs were 2.91 and 0.59 for children and adults, with 85.6% and 13.3% of non-carcinogenic risks for children and adults that exceeded the safe level of 1, respectively. In addition, 70.2% and 56.7% of the total cancer risks through exposure to five carcinogenic PTMs in children and adults, respectively, exceeded the safety level. As and Hg showed a high exceedance of non-carcinogenic risks, while As and Ni were the leading contributors to carcinogenic risks. This study demonstrates the urgent necessity for controlling PTM pollution and reducing the health risks in soils near Hg mining sites and provides an important basis for soil remediation.
● Biosolids boost OM mineralization, enhancing soil health.
● Moderate biosolid doses improve soil conditions effectively.
● SQI w, with Nmin, efficiently gauges soil quality, simplifying monitoring.
Economic development triggers environmental pollution. To address this issue and mitigate its consequences on the environment and human health, urban wastewater treatment plants are commonly employed to produce treated water and biosolids. However, biosolid disposals pose issues due to space limits and leachate contamination. This study investigates the potential of using biosolids as an organic amendment to remediate soil contaminated with leachate from an open dump in Mexico. Treatments with different doses of biosolids were tested (control, without addition of biosolids; high, medium, and low doses, with a C/N = 8, 10, 12 respectively). The physicochemical and biological characteristics of the soil and biosolids were analyzed, and the dynamics of carbon and nitrogen mineralization over time were studied. The developed soil quality index, primarily based on the mineralized nitrogen indicator, differentiated soil quality among treatments, showing values of moderate quality for the treatments (high, medium, and low doses (0.56, 0.48, 0.40, respectively) and low quality for the control (0.34)). The use of biosolids as an organic amendment improved soil quality by increasing organic matter and microbial growth. Soil quality indices emerges as a practical tool for monitoring the remediation of leachate-contaminated open dump soils in Mexico and similar contexts worldwide.
The total arsenic (As) and As species of earthworm body tissues and surrounding soils were investigated in 47 locations (16 forested lands and 31 agricultural lands) at a national scale across China using inductively coupled plasma-mass spectrometer (ICP-MS) and high-performance liquid chromatography-inductively coupled plasma-mass spectrometer (HPLC-ICP-MS). Earthworm body tissues had an average total As concentration of 6.21 mg kg−1, significantly lower than the soil As concentration of 12.99 mg kg−1. The ratio of arsenite to arsenate (AsIII/AsV ratio) in earthworm body tissues (67%) was significantly higher compared to that in surrounding soils (19%). HPLC-ICP-MS analysis detected small amounts of organic As forms, such as arsenobetaine (2.9%), dimethylarsinic acid (1%), and monomethylarsonic acid (0.3%), mainly in earthworm tissues from certain locations. The total As content and AsIII/AsV ratio in earthworm tissues exhibited a strong positive correlation with soil NO3− content. This field study enhances our understanding of As concentration and speciation in earthworm body tissues across China, contributing valuable insights into the biogeochemical cycle of As and its biological risks in diverse soil ecosystems. These findings provide crucial evidence for policymakers to formulate strategies addressing and mitigating soil As pollution and associated health risks.
● P. frumentum biomass could be improved by appropriating returning measures.
● P. frumentum biomass was excellent in 75% alfalfa returning amount.
● Key species of bacteria differed among the alfalfa returning amounts
● The relationship of core bacteria and their potential ecological functions are more close to biomass.
The use of green manure returning to field is a common practice in conservation tillage. However, there is limited research on how different amounts of alfalfa can affect saline-alkali soil properties, bacterial community characteristics, and subsequent productivity. In this study, five different amounts of alfalfa return were investigated to understand the biological relationships between rhizospheres soil properties, bacterial communities, potential functions, and the Purus frumentum biomass. The results showed that the biomass was highest when 75% of the alfalfa was returned to the field. This particular amount was associated with relatively low soil pH and electrical conductivity. Additionally, it increased the relative abundance of beneficial bacterial taxa in both core and non-core bacteria. Statistical analysis revealed significant differences in both core (RANOSIM = 0.871, P = 0.001) and non-core (RANOSIM = 0.947, P = 0.001) bacterial communities among the different amounts of alfalfa return based on non-metric multidimensional scaling analysis. Core bacterial taxa and their potential ecological functions were more closely related to plant biomass compared to non-core bacteria based on correlation analysis and multiple regression analysis. Therefore, our results indicate that optimizing the amount of alfalfa return can improve subsequent plant biomass. Regulating soil physicochemical properties and influencing core microbial community structure are of great significance for soil functional stability and crop productivity sustainability.
● Boreal and temperate forests had higher MNC and FNC/BNC than other forest biomes.
● Mixed forests had higher MNC and lower FNC/BNC than other forest types.
● The dependence of MNC on forest type varied among forest biomes.
● MAT and soil total N were the important factors on MNC and MNC/SOC.
● MAT, soil pH, and clay content were identified as direct factors on FNC/BNC.
Soil microbial necromass carbon (MNC) is an important contributor to soil organic carbon (SOC) and plays a vital role in carbon sequestration and climate change mitigation. However, it remains unclear whether the content, contribution to SOC (MNC/SOC), and fungal-to-bacterial necromass carbon ratio (FNC/BNC) of MNC vary across forest biomes and types. By summarizing data from 1704 points across 93 forest sites, we explored the spatial patterns of MNC, MNC/SOC, and FNC/BNC in the surface layer of 0–20 cm of forest soils, as well as the controlling factors involved. Overall, boreal and temperate forests had higher MNC and FNC/BNC values than tropical, subtropical, and Mediterranean forests, whereas both boreal and Mediterranean forests had low MNC/SOC values. Mixed forests had higher MNC and lower FNC/BNC than broadleaved and coniferous forests, whereas MNC/SOC was higher in broad-leaved forests than that in coniferous forests. Interestingly, the dependence of MNC on forest type also varies among forest biomes. Regression analyses identified soil total N as one of the most important factors affecting MNC and MNC/SOC; whereas MAT, soil pH, and clay content were identified as the important factors affecting FNC/BNC. This synthesis is critical for managing soil MNC to mitigate climate change in forests.
● Soils from Poplar, Willow, Black locust plantations were compared to arable soil.
● Among five tested C cycle functional genes, three discriminated between treatments.
● Fungi contributed more than bacteria to the β-glucosidase enzyme activity.
● Fungal β-glucosidase gene may be considered an indicator of increased C storage.
Soil carbon sequestration is regulated by microbial extracellular enzymes. Insight into this process can be gained by studying the relationship between enzyme activity, soil organic carbon and microbial functional genes. The genetic potential of microorganisms to produce carbon cycling enzymes was evaluated in unmanaged plantations of Poplar, Willow, and Black locust, compared with a nearby arable soil. Bacterial and fungal functional genes encoding for cellulase, endoglucanase, endoxylanase and β-glucosidase enzymes were quantified by real-time PCR. The abundance of three out of five genes differed between the treatments. The fungal gene encoding β-glucosidase contributed to the corresponding enzyme activity more than the bacterial one, as evidenced by a positive correlation between gene abundance and enzyme activity (r = 0.42). This gene exhibited a positive correlation with soil organic carbon content (r = 0.42), with higher values in Willow (9 × 102 gene copies µL−1 and 1.4% SOC). These results suggest that the fungal β-glucosidase gene abundance can be regarded as an indicator of increased carbon storage, similarly to the corresponding enzyme activity. The integrated analysis of soil carbon enzyme activities and DNA-based techniques enhanced our comprehension of carbon dynamics by revealing distinct contributions of microbial taxonomic groups to carbon accrual.
● Ascomycetes of the genus Trichoderma are beneficial fungi that promote plant growth.
● Several fungal species can mitigate abiotic stress in plants.
● Trichoderma spp. induce salt stress tolerance and drought protection in plants.
● Soil contamination by heavy metals can be bioremediated by Trichoderma .
● Trichoderma can detoxify pesticides and other pollutants in soils.
Plants drive both carbon and nitrogen cycling and mediate complex biotic interactions with soil microorganisms. Climate change and the resulting temperature variations, altered precipitation, and water shortages in soils, affect the performance of plants. Negative effects of abiotic stress are reflected in changes of plant morphology associated with biochemical alterations and inadequate adaptation to rapid ecological change. Accumulation of chemical agents, derived from pesticides, salinity due to chemical fertilization, and accumulation of heavy metals, are recurrent problems in agricultural soils. Trichoderma spp. are soil fungi interacting with roots and in this way helping plants to cope with abiotic stresses by increasing root branching, shoot growth and productivity. In part, such fungal effects on the host plant are consequences of the activation of fine-tuned molecular mechanisms mediated by phytohormones, by profound biochemical changes that include production of osmolytes, by the activity of the redox-enzymatic machinery, as well by as complex processes of detoxification. Here, we summarize the most recent advances regarding the beneficial effects of Trichoderma in mitigating the negative effects on plant performance caused by different environmental and chemical factors associated with global change and agricultural practices that provoke abiotic stress. Additionally, we present new perspectives and propose further research directions in the field of Trichoderma-plant interactions when the two types of organism cooperate.
● Core taxa play an important role in regulating soil carbon metabolism.
● Ecological cluster with oligotrophic made key contributions to soil carbon metabolism.
● Microbial cluster characteristics link microorganisms to carbon metabolism.
Characterizing the ecological roles of core soil microbial species in soil carbon metabolism is critically important for enhancing carbon sequestration in agricultural systems; however, no studies to date have determined the effects of core soil microbial taxa on carbon metabolism under various long-term fertilization practices. Here, we collected soil samples from field plots that had been subjected to different fertilization practices for nearly 30 years and examined the long-term effects of fertilization on the preferences of core soil bacterial taxa for different carbon sources. We also examined the relative contribution of core soil bacterial taxa in utilization of different carbon source types in Biolog Eco microplates. Long-term fertilization treatment had a significant effect on soil properties and bacterial community structure. The core taxa were closely related to soil carbon source utilization. The co-occurrence network showed that the major ecological clusters containing core taxa made key contributions to soil carbon source utilization. The organic fertilization increased the abundance of a core cluster with a low weighted average rrn copy number. This ecological cluster was the most important factor affecting soil carbon source utilization even among soil physicochemical factors considered. Our findings indicate that core taxa characterized by oligotrophic bacteria have a major effect on carbon source utilization in Ultisols.
● Under warming soil respiration was higher, but soil microbial biomass was lower.
● Warming effect on soil respiration was higher in soil from the highest elevation.
● Soil respiration was higher in soil with higher soil carbon content.
● Warming increased biomass-specific respiration and enzyme activity.
● The Q 10 did not differ among soils from different elevations.
Global warming is expected to increase the rate of soil carbon (C) efflux through enhanced soil microbial processes, mainly in systems, such as high elevation wetlands, storing large quantities of soil organic C. Here, we assessed the impact of experimental warming on respiration and microbial communities of high Andean wetland soils of the Puna region located at three different elevations (3793, 3862, 4206 m a.s.l.). We incubated soils at 10°C and 25°C for 68 days and measured the soil respiration rate and its temperature sensitivity (Q10). Furthermore, we measured biomass and composition and enzymatic activity of soil microbial communities, and initial and final soil C content. Although warming increased soil respiration rates, with more pronounced effect in soils sampled from 4206 m a.s.l., Q10 did not differ between elevations. Soil C content was higher at the highest elevation. Soil microbial biomass, but not enzymatic activity, was lower for warmed soil samples. However, the biomass-specific respiration and biomass-specific enzymatic activity were higher under warming, and in soil from the highest elevation wetland. These results suggest that, in the short-term, warming could stimulate resource allocation to respiration rather than microbial growth, probably related to a reduction in the microbial carbon use efficiency. Simultaneously, soils with higher soil C concentrations could release more CO2, despite the similar Q10 in the different wetlands. Overall, the soil of these high Andean wetlands could become C sources instead of C sinks, in view of forecasted increasing temperatures, with C-losses at regional scale.
● Refined conversion factors for soil fungal biomarkers are proposed.
● High interspecific variability is present in all fungal biomarkers.
● A modeling approach supports the validity of biomarker estimates in diverse soils.
● ITS1 copies vary strongly, but are fungal-specific with least phylogenetic bias.
● A combination of fungal biomarkers will reveal soil fungal physiology and activity.
The abundances of fungi and bacteria in soil are used as simple predictors for carbon dynamics, and represent widely available microbial traits. Soil biomarkers serve as quantitative estimates of these microbial groups, though not quantifying microbial biomass per se. The accurate conversion to microbial carbon pools, and an understanding of its comparability among soils is therefore needed. We refined conversion factors for classical fungal biomarkers, and evaluated the application of quantitative PCR (qPCR, rDNA copies) as a biomarker for soil fungi. Based on biomarker contents in pure fungal cultures of 30 isolates tested here, combined with comparable published datasets, we propose average conversion factors of 95.3 g fungal C g−1 ergosterol, 32.0 mg fungal C µmol−1 PLFA 18:2ω6,9 and 0.264 pg fungal C ITS1 DNA copy−1. As expected, interspecific variability was most pronounced in rDNA copies, though qPCR results showed the least phylogenetic bias. A modeling approach based on exemplary agricultural soils further supported the hypothesis that high diversity in soil buffers against biomarker variability, whereas also phylogenetic biases impact the accuracy of comparisons in biomarker estimates. Our analyses suggest that qPCR results cover the fungal community in soil best, though with a variability only partly offset in highly diverse soils. PLFA 18:2ω6,9 and ergosterol represent accurate biomarkers to quantify Ascomycota and Basidiomycota. To conclude, the ecological interpretation and coverage of biomarker data prior to their application in global models is important, where the combination of different biomarkers may be most insightful.
● Metals are increasingly important risk factors for the evolution of antibiotic resistance in environments.
The rapid development of antibiotic resistance is occurring at a global scale. We therefore stride into the post-antibiotic era and have to battle antibiotic resistance in the Anthropocene. Metals are widely used and their pollution is widespread worldwide. More importantly, metal-induced co-selection greatly expands the environmental resistomes and increases the health risk of antibiotic resistance in environments. Here, we reviewed the metal-induced co-selection and their increasingly important roles in the development of antibiotic resistance. In particular, we highlight the metal-rich environments that maintain reservoirs for high-risk antibiotic resistance genes with horizontally transferable potentials. We also call for considerations and further investigations of other co-selective agents and the efficacy of metal-based interventions to better manage and combat the global antibiotic resistance crisis within the One Health framework.
In forests, fungal sporocarps house the diverse fungicolous fungi; however, the relationships of sporocarps and associated fungal communities are rarely explored in agroecosystems. In a corn field near Gongzhuling City, Jilin Province, China, we found an epigeous sporocarp with agaricoid morphology that could grow next to the living corn plants. Using PacBio metabarcoding combined with an updated bioinformatic pipeline, we surveyed the fungal community profile along its cap, rhizomorph and hyphosphere soil at a much-improved taxonomic resolution. We identified the sporocarp, at a high probability, as Agrocybe dura, and this mushroom was significantly negatively correlated with Trichoderma hamatum and T. harzianum in the co-occurrence network. Fungal diversity in hyphosphere habitat was significantly higher than that in cap and rhizomorph habitats. Consistent with the pattern in fungal diversity, the node number, edge number, network diameter and average degree were significantly higher in hyphosphere habitat than other habitats. However, both the negative and positive cohesion were significantly higher in rhizomorph habitat than other habitats. Moreover, the z-c plot identified A. dura as the only network hub, linking multiple fungal species. The results give us a glimpse of the ecological relevance of saprobic mushrooms across the extensive northeastern black soil region of China. Our findings will aid in the assessment and forecasting of fungal diversity hotspots and their relationships with soil fertility in the ‘Golden Corn Belt’ of northeast China.
● Fungi outperformed bacterial in maintaining the microbial co-occurrence networks.
● Fungi showed different elevational network co-occurrence pattern from bacteria.
● Distinct biotic/abiotic factors influenced bacterial and fungal network dynamics.
The interplay between soil micro-organisms in mountain ecosystems critically influences soil biogeochemical cycles and ecosystem processes. However, factors affecting the co-occurrence patterns of soil microbial communities remain unclear. In an attempt to understand how these patterns shift with elevation and identify the key explanatory factors underpinning these changes, we studied soil bacterial and fungal co-occurrence networks on Mt. Seorak, Republic of Korea. Amplicon sequencing was used to target the 16S rRNA gene and ITS2 region for bacteria and fungi, respectively. In contrast to bacteria, we found that fungi were predominantly situated in the core positions of the network, with significantly weakened co-occurrence with increasing elevation. The different co-occurrence patterns of fungal and bacterial communities could be resulted from their distinct responses to various environments. Both abiotic and biotic factors contributed significantly to shaping co-occurrence networks of bacterial and fungal communities. Fungal richness, bacterial community composition (indicated by PCoA1), and soil pH were the predominant factors influencing the variation in the entire microbial co-occurrence network. Biotic factors, such as the composition and diversity of bacterial communities, significantly influenced bacterial co-occurrence networks. External biotic and abiotic factors, including climatic and vegetative conditions, had a significant influence on fungal co-occurrence networks. These findings enhance our understanding of soil microbiota co-occurrences and deepen our knowledge of soil microbiota responses to climatic changes across elevational gradients in mountain ecosystems.
● Disease-suppressive soils exhibit enhanced soil nutrient status.
● Soil available phosphorus is a distinct feature of disease-suppressive soil.
● Rhizosphere hosts heightened microbial function for disease suppression.
● The soil microbial role in disease suppression is linked to nutrient cycling.
The role of soil nutrient status in disease suppression is of increasing interest for the control of soil-borne diseases. Here, we explored the soil chemical properties, composition, and functional traits of soil microbiomes in pair-located orchards that appeared suppressive or conducive to the occurrence of banana Fusarium wilt using mainly amplicon sequencing and metagenomic approaches. The enhancement of soil available phosphorus, succeeded by increments in soil nitrogen and carbon, played a pivotal role in the suppression of the disease. Additionally, in therhizosphere of suppressive sites, there was an observed increase in the disease-suppressing function of the soil microbiome, which was found to be correlated with specific nutrient-related functions. Notably, this enhancement involved the presence of key microbes such as Blastocatella and Bacillus. Our results highlight the significant roles of soil nutrient status and soil microbiome in supporting the soil-related disease suppressiveness.
● Community structure and composition of AMF shifted under different fertilization.
● Soil physicochemical properties played important roles in contributing plant diversity and biomass.
● Fertilization affected plant and AMF communities through changing soil abiotic properties.
● Acaulospora and Diversispora were highly linked with plant communities.
Arbuscular mycorrhizal fungi (AMF) represent a crucial component of soil microorganisms, playing pivotal roles in promoting plant growth by enhancing nutrient availability. However, the responses of AMF communities to different fertilization regimes and their correlations with plant communities in the context of anthropogenic disturbances in alpine meadow ecosystems remain largely unexplored. In this study, we investigated the effects of nitrogen, phosphorus, and combined nitrogen-phosphorus fertilization on AMF communities and their interconnections with plant diversity and biomass based on a seven-year long-term experiment conducted on the Qinghai-Tibet Plateau. Our results showed significant shifts in AMF community structure and composition under different fertilization treatments, while the richness of AMF exhibited no remarkable alterations. Notably, soil pH decreased, and electrical conductivity increased with the increasing nitrogen fertilizer application, emerging as pivotal abiotic factors in predicting plant richness and biomass. Fascinatingly, Acaulospora exhibited a positive correlation with plant richness, serving as an important bioindicator of plant richness, while Diversispora emerged as the primary bioindicator of plant biomass. Our findings shed light on potential correlations between AMF community composition and both plant and soil abiotic factors, driven by nitrogen and phosphorus fertilization. We advocate for the critical significance of balanced fertilization in sustaining beneficial plant–soil–AMF interactions in natural ecosystems as well as agricultural soils.
● Tourism development influenced the ecological network of microbial communities.
● Regulating mechanism of intra- and inter-domain networks was clarified.
● Macrophyte coverage reduces microbial network complexity and stability.
● Landscaping may promote nitrogen and phosphorus cycle in wetland watershed.
Numerous urban wetland parks have been established, yet the understanding of microbial interactions in response to tourism development is still limited. This study aims to elucidate the impact of tourism development on the complexity and stability of molecular ecological networks within the microbial communities of wetland sediments. Through an analysis of sediments properties, microorganism intra- and inter-domain co-occurrence characteristics in three different wetland functional areas (conservation, landscaping, and recreation areas), we found that tourism development influenced sediment physicochemical properties. These changes regulated the diversity and ecological networks of archaeal and bacterial communities. Specifically, areas with landscaping (LA) exhibited reduced network connectivity and robustness, suggesting that macrophyte coverage diminishes the complexity and stability of microbial communities in wetland parks. Notably, the transition from conservation areas (CA) to LA strengthened the correlations between microbial network modules and sediment total nitrogen (TN) and total phosphorus (TP), potentially enhancing the nitrogenand phosphorus cycles in wetlands. Structural equation modeling analysisrevealed that both abiotic factors (TC, TP, TN, K, Mg, pH) and biotic factors (archaeal and bacterial α-diversity) can influence interdomain network complexity, accounting for 42% of the variation. Among these factors, sediment TN exerted the largest positive effect on network complexity (37.9%), while Mg had the most negative impact (59.8%). This study provides valuable insights for ecological assessments of urban wetlands and can inform strategies for effective wetland ecosystem management.
● Soil respiration rates ( R s) were measured in New Zealand dairy grassland.
● Both season and soil type significantly affected R s.
● Soil temperature and soil type dominated overall R s.
Soil respiration (Rs), the CO2 release from root respiration and microbial metabolism, affects global soil carbon storage and cycling. Only few studies have looked at Rs in the southern hemisphere, especially regarding the interaction between soil type and environmental factors on Rs in dairy grassland. We investigated the relationship between Rs and soil temperature (Ts), soil water content (SWC), soil type, and other environmental factors based on summer and winter measurements at four sites in New Zealand. Across sites, soil respiration rates ranged from 0.29 to 14.58 with a mean of 5.38 ± 0.13 (mean ± standard error) µmol CO2 m−2 s−1. Mean summer Rs was 86.5% higher than mean winter Rs, largely driven by organic/gley and pumice soils while ultic soils showed very little seasonal temperature sensitivity. Overall mean Rs in organic/gley soils was 108.0% higher than that in ultic soils. The high Rs rate observed in organic/gley was likely due to high soil organic matter content, while low Rs in ultic and pallic soils resulted from high clay content and low hydraulic conductance. Soil temperature drove overall Rs. Our findings indicate that soil type and soil temperature together best explain Rs. This implies that a mere classification of land use type may be insufficient for global C models and should be supplemented with soil type information, at least locally.
● We estimated the effect of three crop strategies on soil health based on 63 functional genes in long-term fields.
● The keystone microbial phylotypes support the agroecosystem sustainability.
● Rotation management thrives keystone phylotypes and soil functions.
● Rotation with soybean is beneficial for the subsequent crops.
Given the often-independent study of microbial diversity and function, the comprehensive impact of various cropping patterns on both aspects, as well as the interconnections between them, remains unclear. This gap constrainsus from evaluating the impact of soil microbiome shifts on soil health across varying agricultural management regimes. Here, we examined the associations between microbial diversity and soil multifunctionality in three long-term cropping patterns: continuous soybean cropping, soybean-corn rotation, and continuous corn cropping. We targeted 63 functional genes associated with carbon, nitrogen, phosphorus and sulfur cycling to assess soil multifunctionality. Our study demonstrated that the biodiversity and interactions of keystone phylotypes had significant positive associations with multiple soil functional genes, such as organic carbon degradation and fixation, nitrogen fixation and phosphorus solubilization. The analysis of retrieved complete genome revealed that the keystone bacteria identified in our study harbored these functional genes. Moreover, these keystone phylotypes showed associations with the dissipation of herbicide residues. Above all, we revealed that rotation of soybean with corn cropping enhanced a greater diversity of keystone phylotypes and thus fueled soil functions. Collectively, our results highlighted the importance of rotation with soybean in maintaining soil health, which could give a mechanism-based guidance for a sustainable agroecosystem.
● Compound biological bait can replace commercial bait to ensure fish growth.
● The compound biogenic bait can effectively improve the water and soil environment.
● The key microbiome induced by compound biogenic bait plays an important role.
Traditional commercial aquatic fish bait (CA) is not conducive to the scientific breeding of rice and fish in cocropping systems, and excessive feeding easily causes environmental pollution in rice fields. In this study, an environment-friendly compound biogenic bait (CB) mixed with plant-derived (PB) and animal-derived (AB) baits was proposed. The rice–crucian carp cocropping system was used as the research object, and the soil microorganisms and fish gut microorganisms were sequenced with high throughput, respectively, to verify the effect of CB application and the microbial mechanism underlying its functional effect. The results showed that the AB and PB components in CB maintain the growth of fish by improving the metabolism-related functions of fish gut microbiome and reducing the abundance of intestinal pathogenic bacteria, including Actinomadura. In particular, the PB components induced soil microbiome, such as Pseudonocardia, that participate in soil nutrient cycling and increase dissolved oxygen in water, which is key for improving rice quality and yield. This is the first study to focus on how different bait components drive key microbial communities to regulate animal–plant–environment relationships in the integrated planting and breeding patterns of paddy fields.
● Egg hatching of the soil collembolan Folsomia candida and the effects of per- and polyfluoroalkyl substances were investigated.
● New and effective laboratory methods for egg hatching studies with soil collembolans were established.
Per- and polyfluoroalkyl compounds (PFASs) have been used industrially worldwide and are persistent organic pollutants in many soils. Twenty eggs laid by synchronized adults of the collembolan Folsomia candida were added to each Petri dish containing compressed soil substrate mixed with perfluorooctanoic acid (PFOA), heptafluorobutyric acid (PFBA), or 6:2 chlorinated polyfluoroalkyl ether sulfonic acid (F-53B), and after 25 d of exposure the number hatched declined on average by 6.9%−49.7%, 10.3%−24.1%, and 3.4%−18.6%, respectively. PFASs delayed the peak of hatching by one day, and at different concentrations reduced the number of eggs hatched during the peak by 16.7%−30% and 23.3%−43.2% in PFOA and PFBA treatments, respectively. In the presence of F-53B the number of eggs hatched declined by 73.3% but the number of individuals increased by 29.3% at higher concentrations. The characteristics of egg hatching were stable and sensitive to PFASs, and may be suitable for use as indicators in the screening of contaminated soils for environmental risk assessment.
● Bacterial and fungal necromass in soil showed opposite trends with rice growth.
● The contribution of GRSP increased but ASs decreased to SOC with rice growth.
● Microbial residues were mainly influenced by living microbial biomass.
Microbial residues play an important role in soil organic carbon (SOC) sequestration. Paddy fields are important agricultural ecosystems involved in the carbon cycle; however, microbial residues change with rice growth in soil from double-season rice, and the influence of these residues on SOC sequestration is uncertain. Here, we investigated the microbial residues (amino sugars (AS) and glomalin-related soil protein (GRSP)) content and their contribution to SOC during the tillering stage (TS), heading stage (HS), and ripening stage (RS) in both early- and late-season rice in a double-cropping rice-growing area wherein the straw is returned after the early-season rice is harvested. Microbial biomass significantly increased from the early- to the late-season. In addition, the content of bacterial residues decreased (7.94%, P=0.008), while the fungal residues increased (8.15%, P<0.001) in the late-season compared with the early-season, suggesting that bacterial residues were recycled more rapidly than fungal residues. Amino sugar content and its contribution to SOC decreased from the TS to the RS in the late-season soil, probably because of the nutrient requirements of the rapidly growing rice. The contribution of GRSP to SOC increased by 10.5%, whereas that of ASs decreased by 4.5% from the early- to the late-season. Living soil microbes rather than soil physicochemical properties were the main factors influencing microbial residue accumulation. The results of this study provide a theoretical basis from a microbial perspective which will facilitate future efforts to enhance SOC sequestration during paddy field management.
● Earthworms significantly reduced soil CH4 uptake at both temperatures, and warming significantly promoted soil CH4 uptake.
● Earthworms significantly altered methanotroph community, and warming significantly altered methanogen community, and their interaction had a significant influence on both methanogen and methanotroph communities.
● Soil properties exhibited a negative impact on CH4 uptake, while the α-diversity of methanotrophs was associated with enhanced CH4 uptake.
● Dissolved organic carbon (DOC) was identified as the most essential factor in forecasting soil CH4 uptake.
The function and service of biologically driven ecosystems are undergoing significant changes due to climate warming. Earthworms play a crucial role as soil engineer by modulating the effects of climate change on soil nutrient cycle through alterations to biotic and abiotic soil conditions. However, there is currently a scarcity of information regarding the impacts of earthworms and warming on soil CH4 uptake and their associated microbial mechanisms. This study conducted a 61-day microcosm experiment to investigate the impact of warming (temperature rise from 14.2 °C to 17.2 °C) and the presence of earthworms (Eisenia fetida and Moniligaster japonicus) on soil CH4 uptake. We employed gas chromatography and high-throughput sequencing to investigate the fluctuations in soil CH4 uptake and the microbial communities involved in methane cycling. Compared to low temperature conditions (14.2 °C), we observed that warming significantly increased soil CH4 uptake in all treatments (non-earthworm: 51.85%; Eisenia fetida: 50.88%; Moniligaster japonicus: 71.78%). Both Eisenia fetida and Moniligaster japonicus significantly reduced soil CH4 uptake at two temperatures compared to the non-earthworm treatment. Nevertheless, no significant impacts were found on soil CH4 uptake due to the interactions between earthworms and warming. The methanotroph communities exhibited notable variations among earthworm treatments, whereas the methanogenic communities displayed significant differences among temperature treatments. The interaction between earthworm and warming also resulted in noticeable variations in both methanogenic and methanotrophic communities. The FAPROTAX analysis revealed that earthworms and warming altered relative abundance of methanogens and methanotroph associated with CH4 cycle functions. Soil properties exhibited a negative impact on CH4 uptake, with DOC identified as the most crucial variable in predicting soil CH4 uptake, while the α-diversity of methanotrophs was associated with enhanced CH4 uptake. This study emphasized the crucial role of soil fauna in adjusting soil greenhouse gas emissions under the context of global warming.
● Moderate dilution of natural soil with clay mineral complexes generated oligotrophic soils with a gradient of microbial abundance but similar C availability.
● In contrast to the regulatory gate hypothesis, small changes in microbial abundance strongly influenced soil C decomposition despite similar C availability.
The regulatory gate hypothesis suggests that the mineralization of soil organic matter (SOM) is controlled by carbon accessibility due to microbial redundancy. However, this opinion is contentious because the extensively high available carbon released during the fumigation in these studies strongly stimulated microbial activity, which is unlikely to occur in real soil and would compensate for the effect of reduced microbial abundance. In this study, natural soil was moderately diluted with mineral complexes in varying proportions to obtain soils with a gradient of microbial abundance and low carbon availability. The results revealed that despite minimal changes in the dissolved organic carbon content (DOC), the CO2 emission rate and activity of SOM hydrolysis significantly decreased with decreasing microbial abundance. Regression analysis and the random forest model highlighted microbial abundance as the primary factor influencing carbon decomposition, which was more fundamental than DOC and microbial diversity. These findings underline the crucial role of microbes in soil carbon turnover and the importance of maintaining microbial abundance to preserve the soil carbon cycling capacity.
● The Transformer model precisely predicts soil health status from high-throughput sequencing data.
● The SMOTE algorithm addresses data imbalance issues, improving model accuracy.
● Transfer learning validates the model on small samples, strengthening its generalization capabilities.
Inhibiting the occurrence of soil-borne diseases is considered as the most favorable approach for promoting sustainable agricultural development. Constructing soil disease prediction models can serve precision agriculture. However, the analysis results of the meta-framework often contradict each other, causing inconsistency in the important features of machine learning results. Therefore, it is necessary to compare the classification accuracy of various machine learning models and further optimize the features of the models to enhance their classification accuracy. Here, we conducted a comparison of eight common machine learning algorithms (XGBoost, CatBoost, Decision Tree, LGBM, Naïve Byes, Perceptron, Logistic, and Random Forest) at the levels of family, genus, and class. The important features of the model were extracted based on the differences in model accuracy and important features, followed by an interpretable analysis of these important features using feature importance. Subsequently, the data underwent resampling using the SMOTE algorithm, and the results show that the SMOTE-Transformer model performs well, surpassing the training results of the voting and stacking strategies, with an accuracy reaching 90%. We have also deployed the SMOTE-Transformer model on sequencing data, which has an accuracy of over 80%. The construction of SMOTE-Transformer model provides a new idea for soil microbial data analysis by greatly improving the accuracy and robustness of soil microbial data processing tools.
● Rhizosphere microbial network in crater had higher complexity than in volcanic cone.
● Bacteria were more prone to enrichment than fungi in volcanic soils.
● The bacteria exhibited greater resistance and resilience than fungi.
Volcanic eruptions are significant natural disturbances that provide valuable opportunities to study their impacts on soil microorganisms. However, no previous studies have compared the rhizosphere microbial communities of Boehmeria nivea L. in volcanic craters and cones. To address this gap, we conducted a comprehensive investigation using Illumina MiSeq high-throughput sequencing to compare the rhizosphere microbial communities in volcanic craters and cones. Principal Coordinate Analysis revealed significant differences in the rhizosphere microbial communities between the crater and cone. The bacterial communities in the rhizosphere of the crater exhibited higher diversity and evenness compared to the cones. Moreover, the cones displayed more intricate bacterial networks than the crater (nodes 556 vs. 440). Conversely, fungal networks were more complex in the crater than the cone (nodes 943 vs. 967). Additionally, bacterial communities demonstrated greater stability than fungal ones within these volcanic soils (avgK 241.1 vs. 499.7) and (avgCC 1.047 vs. 1.092). Furthermore, the Structural Equation Model demonstrated a direct positive impact of alpha diversity on soil microbial community multifunctionality in the crater (λ = 0.920, P < 0.001). Our findings have presented the opportunity to investigate the characteristics of the rhizosphere microbial communities of Boehmeria nivea L. in the crater and cone.
